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SIBO: What Causes It & How to Treat It

Written by Mathew Eng, PharmD | Last updated:
Nattha Wannissorn
Puya Yazdi
Medically reviewed by
Nattha Wannissorn, PhD, Puya Yazdi, MD | Written by Mathew Eng, PharmD | Last updated:

Small intestinal bacterial overgrowth (SIBO) can cause constipation, diarrhea, malnutrition, unexplained weight loss, and fatigue. Find out what causes it, how to test for it, and what the treatments are.

What is SIBO?

Small intestinal bacterial overgrowth (SIBO) is a condition where there is an excessive amount of bacteria in the small intestines. Normally, the small intestines contain a small population of “good” bacteria that help with digestion and the immune system [1].

A large increase in the number of bacteria or the presence of abnormal bacteria can cause SIBO, which can cause several symptoms, including bloating, diarrhea, and abdominal pain [1].

This overgrowth of bacteria can also disrupt the body’s ability to absorb nutrients, often leading to nutrition deficiencies [1].

There are several potential causes of SIBO, such as decreased movement in the digestive system, structural abnormalities in the gut, and certain medications [1].

Symptoms of SIBO

SIBO can cause a variety of diverse symptoms which include [2]:

  • Constipation
  • Bloating
  • Flatulence
  • Diarrhea
  • Nausea
  • Abdominal pain
  • Malabsorption and Malnutrition
  • Weight Loss
  • Fatigue
  • B12 deficiency
  • Leaky gut
  • Rashes
  • Joint pain
  • Depression

Because these are general, nonspecific symptoms, it can be hard to tell the difference between SIBO and other conditions such as IBS, lactose intolerance, or fructose intolerance.

Causes of SIBO

SIBO can be caused by many factors and conditions.

These can be broken down into three distinct groups [2]:

  • Disorders of the gut’s antibacterial mechanisms
  • Structural abnormalities
  • Disorders that cause slow digestion

1) Disorders of Antibacterial Mechanisms

The digestive system has ways to prevent the overgrowth of bacteria, such as stomach acid, bile, enzymes, and immune cells. A lack of any of these allows bacteria to thrive, potentially leading to SIBO [3].

Low Stomach Acid and Enzyme Production

Stomach acid destroys bacteria before they reach the small intestine. A lack of acid production allows bacteria to pass through the stomach into the small intestine where they can potentially multiply. Enzymes released from the pancreas also help destroy bad bacteria in the small intestine [2].

Health conditions or medications that disrupt the stomach’s ability to secrete acid may increase the risk of SIBO [1].

Lack of Bile Flow

Bile acids can inhibit bacterial growth in the small intestine. When bile production in the liver or flow from the gallbladder decreases, pathogenic (“bad”) bacteria in the small intestine can increase [4].

Underactive Immune System in the Gut

Conditions that impair the body’s immune system can lead to bacterial growth in the small intestine.

For example, SIBO is common in people with a genetic condition that causes a lack of IgA, a type of antibody that helps detect and eliminate bacteria. Bacterial overgrowth is also common in AIDS patients due to an underactive immune system [5, 6].

2) Structural Abnormalities

Structural flaws in the small bowel can lead to SIBO. This happens because certain structural abnormalities trap bacteria and allow them to accumulate.

Small Intestinal Inflammation

Diverticula are small pouches in the small intestine that can become inflamed. These pouches can collect bacteria and lead to SIBO [1].

One study of 90 people found that 59% of the patients with diverticulitis had SIBO [7].

Bad Connections Between Intestine and Organs

Intestinal fistulas are unnatural connections between an organ and the intestines. Bacteria can become trapped in these connections, potentially leading to SIBO [1].

Ileocecal Valve Dysfunction

The ileocecal valve separates the end of the small intestine from the beginning of the large intestine. When this valve is damaged or removed, bacteria can travel from the large intestine back into the small intestine. Research shows that bacterial overgrowth often occurs soon after patients have their ileocecal valve removed [8, 9].

Stomach and Gut Surgeries

Stomach and gut surgeries such as gastric bypass surgery can potentially cause SIBO. Stomach and gut surgeries that bypass parts of the gut can create sections that collect bacteria called blind loops. Because SIBO often develops in people who have these blind loops, it is often referred to as Blind Loop Syndrome (BLS) [1].

3) Disorders Causing Slow Digestion (Gut Flow Disorders)

Normally, the muscles lining the stomach and small intestine will contract and relax in waves. This process is known as the migrating motor complex (MMC). The MMC stops bacteria in the colon from coming up into the small bowel [10].

Peristalsis is the movement of food down the gut caused by wavelike contractions of muscles lining the gut. It occurs whether food is present or not.

Any disease or disorder that stops the MMC or slows peristalsis will let bacteria from the large intestine travel into the small intestine.

Diabetic neuropathy

Diabetic neuropathy is damage to the nerves of the gut from diabetes. When the nerves become damaged (because of high blood sugar), gut movement may slow down, allowing bacteria to accumulate.


Scleroderma is a chronic connective tissue disease. It partially blocks the intestines, slowing down the movement of food. This also allows bacteria to accumulate.

Research has found SIBO to be present in 43 – 56% of scleroderma patients [11, 12].

Other Causes

Overconsumption of Alcohol

Heavy alcohol use has been associated with SIBO. Even moderate alcohol consumption (1 drink/day for women, 2 drinks/day for men) has been linked to lead to SIBO. Alcohol can damage the gut in several different ways, including [13]:

  • Decreases enzymes
  • Damages the villi
  • Thickening of the gut wall with connection tissue (fibrosis)
  • Slows gut movement
  • Decreases immune system activity in the gut

Some “bad” types of bacteria may even be able to feed off alcohol. All of these factors may lead to bacterial overgrowth [14].

Overconsumption of Refined Carbohydrates

Diets rich in refined sugars tend to increase the growth of bacteria, both good and bad. The body can only absorb so much sugar at once and any extra sugar may be used by opportunistic bacteria. SIBO patients can also sometimes have less of the enzymes needed to break down and absorb sugars, leaving them to be absorbed by bacteria [15, 1, 16].

Common Risk Factors

The following have been associated with a higher risk of developing SIBO:

  • Use of proton-pump inhibitors (PPIs) and other antacids [17]
  • Use of painkillers [17]
  • Lack of breastfeeding [18]
  • Antibiotic use [1]
  • Age [1]
  • Celiac Disease [19]
  • Crohn’s Disease [19]
  • IBS [1]
  • Liver diseases [1]
  • Kidney Failure [1]
  • Inflammation of the pancreas [1]
  • Leaky Gut [20]
  • Immunodeficiency [17]
  • Diabetes Mellitus (type I and type II) [17]

Is SIBO Linked to Other Diseases?

1) Irritable Bowel Syndrome (IBS)

Research suggests that SIBO is present in 30 – 85% of patients with irritable bowel syndrome (IBS). In a randomized placebo-controlled trial of 111 patients with IBS, treatment with the antibiotic neomycin improved their symptoms (DB-RCT) [21, 2, 22].

The prevalence of SIBO in celiac patients varies between 50 – 75%, according to studies [23, 24].

2) Inflammatory Bowel Disease

Studies show that SIBO is present in 25 – 33% of patients with Crohn’s disease [25, 26, 27].

Small bowel overgrowth is also linked to ulcerative colitis (UC). One study found bacterial overgrowth in ~18% of UC patients [22].

3) Rosacea

One study of 113 patients found SIBO in 46% of rosacea patients [28].

4) Fibromyalgia

In a study of 42 patients with fibromyalgia, all of the patients tested positive for SIBO. The severity of the overgrowth was linked to the degree of pain [22].

5) Other Diseases

There is some evidence that SIBO may be linked to several other diseases, including [29, 30, 31, 32, 33]:

  • hypothyroidism
  • non-alcoholic fatty liver disease
  • rheumatoid arthritis
  • cirrhosis of the liver

How To Test

There are two types of tests commonly used to diagnose SIBO:

  • jejunal aspiration
  • hydrogen breath test (HBT)

Sampling The Small Intestine

The gold standard for SIBO testing is a jejunal aspiration. This involves taking a sample from the small intestine and counting the number of bacteria per mL.

However, this test can be costly and invasive because it requires a tube to be inserted into the small bowel [1].

Hydrogen/Methane Breath Test

Breath tests are a more popular way to diagnose SIBO due to its low risk, simplicity, and noninvasive nature compared to jejunal aspiration.

The test involves the patient fasting overnight and then eating a sugar that is fermented by the bacteria in the small intestine. The gases from the bacteria are then captured and used to see if there is an overgrowth [1].

HBT has its drawbacks. In about 15 – 30% of people with SIBO, the bacteria will produce methane instead of hydrogen [34].

It is necessary to also test for methane if the hydrogen breath test is negative. People who test positive for methane tend to have constipation [35, 21, 36].

The HBT also has a high false-negative rate. This means that the test turns up a negative result when in fact the person does have SIBO [20].

Lastly, there is no consensus as to what determines a positive result. The only way of being confident in the results is to treat SIBO and see if symptoms disappear [1].

Treatments for SIBO

Below we’ll discuss some of the treatments commonly used to help treat SIBO. Usually, the underlying cause of SIBO must also be addressed. Always talk to your doctor if you suspect you may have this condition. Do not try to use any of these treatments without the guidance of a medical professional.


Antibiotics are typically the first-line treatment in SIBO. Several different kinds of antibiotics may be used, but the most well-researched medication is rifaximin [1].

A meta-analysis of 10 clinical trials found that antibiotics, in general, are more effective for treating SIBO compared to placebo [37].

A systematic review of 32 trials including 1,331 patients suggests that rifaximin is safe and effective for the treatment of SIBO, although the quality of studies was generally poor [38].


Probiotics are also often used to manage SIBO. Probiotics contain “good” bacteria that may help balance the population of bacteria in the gut.

A systematic review of 18 studies suggests that probiotics may reduce abdominal pain and help eliminate SIBO. However, the researchers also found that probiotics are ineffective at preventing SIBO [39].

Elemental Diets

Patients with SIBO are sometimes placed on special diets to help manage the condition.

An elemental diet is a liquid diet that consists of the individual nutritional parts of food such as:

  • amino acids
  • fats
  • sugars
  • vitamins
  • minerals

It’s given to patients with inflammatory bowel diseases because the nutrients don’t need to be digested and are absorbed easily.

Elemental diets starve bacteria because they are low in carbohydrates that the bacteria in the small intestine eat.

In a study of 93 IBS patients with SIBO, 15 days of an elemental diet resulted in normal breath tests for 80% of the patients [40].

However, there are some drawbacks to this diet. Elemental formulas do not taste pleasant and can be challenging to stay on for long enough. Indeed, 25% of subjects refuse to stay on the diet for more than 2 – 3 weeks, according to research [41].

About the Author

Mathew Eng

Mathew Eng

Mathew received his PharmD from the University of Hawaii and an undergraduate degree in Biology from the University of Washington.
Mathew is a licensed pharmacist with clinical experience in oncology, infectious disease, and diabetes management. He has a passion for personalized patient care and believes that education is essential to living a healthy life. His goal is to motivate individuals to find ways to manage their chronic conditions.


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